TASSEL 5

TASSEL project is a Java platform designed for the optimized analysis of crop genomic diversity.

User Documentation

• Reporting Tassel 5 Issues

• Tassel 5 User Manual

• Getting Started with rTASSEL

• R front-end for TASSEL (rtassel)

• Tassel 5 GBS v2 Pipeline

• Installing / Updating Tassel using Git (recommended)

• Executing Tassel

• Tassel 5.0 Pipeline (Command Line Interface)

• Tassel 5 Pipeline Tutorial

• Tassel Pan-genome Atlas (PanA) Pipeline

• Tassel VCAP Documentation

Developer Documentation

• Programming Reference URLs

• IntelliJ Setup

• PyCharm Setup for Kipoi

• Eclipse Setup

• Netbeans Setup

• Git: Branches and Pull Requests

• Guide for programming

• Tassel 5 Architecture

• Tassel 5 JavaDoc

• Releasing Tassel 5 and PHG

• Creating Tassel Build from Source Code

• Tassel 5 Logging

• Executing Tassel 5 Unit Tests

• Tassel 5 Self-Describing Plugins

• Testing Tassel with JUnit

Archived User Documentation

• Tassel 3.0 and 4.0 Pipeline (Command Line Interface)

• Tassel 3 Pipeline Tutorial

• Tassel GBS Pipeline

• Tassel UNEAK Pipeline

• Tassel and R Integration

Example Java Code

• Reading/writing hapmap, manipulating genotype tables, writing to text file

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